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X-ray high resolution structure of the photosynthetic reaction center from Rb. sphaeroides at pH 6.5 in the neutral state, 2nd dataset
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PCR PDB ENTRY 1PCR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 pH 6.5
Crystal Properties Matthews coefficient Solvent content 4.75 73.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.451 α = 90 b = 139.451 β = 90 c = 184.393 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH MIRROR 2002-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.04 25 98 0.06 18.36 3.9 128457 -3 36.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.06 98.5 0.57 3.07
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PCR 2.04 119.52 124861 2575 97.2 0.208 0.208 0.1985 0.232 0.1983 RANDOM 42.17
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.531 r_scangle_it 3.283 r_angle_refined_deg 2.44 r_scbond_it 2.172 r_mcangle_it 1.414 r_mcbond_it 0.795 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.204 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.531 r_scangle_it 3.283 r_angle_refined_deg 2.44 r_scbond_it 2.172 r_mcangle_it 1.414 r_mcbond_it 0.795 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.204 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.121 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6471 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 794
Software Software Software Name Purpose REFMAC refinement HKL data reduction SCALEPACK data scaling CNS phasing